He was supposedly killed during the outbreak in the Super-Sized Electromagnetic Distribution Coil control room in the Machine Hall, where Aubrey is stranded. With no other company and in an attempt to not go insane, Aubrey pretends to have discussions with Benny's deceased body and even uses his decapitated arm as a back scratcher.
It is later learned that Benny was not killed due to the outbreak, but was murdered by Aubrey presumably due to Aubrey's frustration with his workers reaching a climax. in various notes it is revealed that the maintenance workers were incompetent ( and were likely Edison spies ) and caused disasters every day and Aubrey despised them to the point of casually referring to them as "assholes" and later "defective fucks". several times Rose sees visions of workers being rallied by a foreman implying that after Benny's death they trapped Aubrey in the control room or rather in self defense Aubrey trapped himself.
It is likely that his name is not Benny at all, but a nickname made up by Aubrey. No know passenger of the Helios has the name Benny or Benjamin further implying his spy status.
Throughout the game, Aubrey contacts Rose Archer via the radio and will continuously refer and talk to Benny as if he was alive. Occasionally Rose can eavesdrop on their one-sided discussions when the transmission is turned on by accident.
When Rose arrives at the control room, she will find Benny's body in a chair. He is severally bloodied and has a sign with the text "Benny" on him. His decapitated arm is found next to him on the floor.
In the Main Garden, Rose sees various "flashes" of past and future events, including Aubrey attacking and murdering an unprovoked Benny.